The cross-border pursuit of bicycle thieves, piglet rustlers and those accused of trivial offences is damaging the credibility of the European arrest warrant, according to a report from Brussels.

The warning from the EU justice commissioner, Viviane Reding, comes amid calls for the introduction of a threshold below which extradition would not be permitted for minor allegations.

Poland, in particular, has become notorious among EU states for the large quantity of its warrants. The Home Office has lobbied for a change to reduce the law enforcement burden.

The European arrest warrant (EAW) was introduced in January 2004 as a means of speeding up extraditions between EU states. Among those currently resisting removal is Julian Assange, the WikiLeaks founder, who is facing allegations of rape and sexual assault in Sweden.

The warrants have been criticised by Fair Trials International for permitting a "disproportionate infringement of basic rights". According to the organisation, the UK received 2,403 requests from Poland last year.

Addressing such concerns in the commission's reporton Monday, Reding said: "The European arrest warrant is an important tool to catch criminals, but member states should ensure that it is used correctly.

"European arrest warrants should not be issued mechanically, or automatically, for crimes that are not very serious such as bicycle theft. The national governments need to build up trust between their judicial systems so that the European arrest warrant works even more efficiently."

Nearly 55,000 EAWs were issued between 2005 and 2009, the report says. Among the successes it highlights is the return from Spain of dozens of British suspected drug smugglers, murderers and child sex crime offenders. Under Operation Captura, led by the Serious Organised Crime Agency, more than 40 suspects have been brought back to face justice in British courts, mainly through the use of EAWs.

"The arrest warrant has had a marked effect in speeding up the transfer of suspected offenders between EU countries," the report notes. "Extradition before the arrest warrant used to take an average of one year, but this has now been cut to 16 days when the suspect agrees to surrender, or 48 days when they do not."

The report adds: "Confidence in the EAW has been undermined by the systematic issue of EAWs for the surrender of persons sought in respect of often very minor offences."

The Labour MEP Claude Moraes, who speaks on justice and home affairs for the socialist group in the European parliament, welcomed the report but said: "There has to be a compulsory threshold. If member states will not introduce it then it should be done at EU level.

"The issue of trivial offences is being taken up by eurosceptics. EAWs have been sought for bicycle thefts and stealing piglets. The phalanx of trivial cases is in danger of drowning out the good cases."

The European commission is introducing procedural changes to ensure that suspects are guaranteed rights to an interpreter and access to a lawyer.

Figures released recently by the Home Office in reply to a question by the Labour MP Caroline Flint show that out of 699 individuals "surrendered" by the UK to other EU states under EAWs, nearly two-thirds (425) were sent to Poland. Other east European states also had large numbers: Lithuania 55, the Czech Republic 34 and Romania 18.

There appears to be a legal standoff between the commission and member states about who should introduce a threshold allowing only serious crimes to be pursued through EAWs. The EC is reluctant to redraft its regulations because it fears opening up a Pandora's box of competing reforms.

The UK is one of the countries criticised for not making changes to its domestic legislation. Fair Trials International has called for legislative change in Brussels incorporating a threshold test in the warrant so that it could not be used for minior offences.